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Posted to commits@airavata.apache.org by sh...@apache.org on 2015/06/03 20:14:44 UTC
[27/39] airavata git commit: Refactored gfac sub modules,
merged gfac-ssh, gfac-gsissh, gfac-local,
gfac-monitor and gsissh modules and create gface-impl,
removed implementation from gfac-core to gfac-impl
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Cluster.java
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diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Cluster.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Cluster.java
new file mode 100644
index 0000000..beb5b37
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Cluster.java
@@ -0,0 +1,162 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.ssh.api;
+
+import java.util.List;
+import java.util.Map;
+
+import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
+import org.apache.airavata.gfac.ssh.impl.JobStatus;
+
+import com.jcraft.jsch.Session;
+
+/**
+ * This interface represents a Cluster machine
+ * End users of the API can implement this and come up with their own
+ * implementations, but mostly this interface is for internal usage.
+ */
+public interface Cluster {
+
+ /**
+ * This will submit a job to the cluster with a given pbs file and some parameters
+ *
+ * @param pbsFilePath path of the pbs file
+ * @param workingDirectory working directory where pbs should has to copy
+ * @return jobId after successful job submission
+ * @throws SSHApiException throws exception during error
+ */
+ public String submitBatchJobWithScript(String pbsFilePath, String workingDirectory) throws SSHApiException;
+
+ /**
+ * This will submit the given job and not performing any monitoring
+ *
+ * @param jobDescriptor job descriptor to submit to cluster, this contains all the parameter
+ * @return jobID after successful job submission.
+ * @throws SSHApiException throws exception during error
+ */
+ public String submitBatchJob(JobDescriptor jobDescriptor) throws SSHApiException;
+
+ /**
+ * This will copy the localFile to remoteFile location in configured cluster
+ *
+ * @param remoteFile remote file location, this can be a directory too
+ * @param localFile local file path of the file which needs to copy to remote location
+ * @throws SSHApiException throws exception during error
+ */
+ public void scpTo(String remoteFile, String localFile) throws SSHApiException;
+
+ /**
+ * This will copy a remote file in path rFile to local file lFile
+ * @param remoteFile remote file path, this has to be a full qualified path
+ * @param localFile This is the local file to copy, this can be a directory too
+ * @throws SSHApiException
+ */
+ public void scpFrom(String remoteFile, String localFile) throws SSHApiException;
+
+ /**
+ * This will copy a remote file in path rFile to local file lFile
+ * @param remoteFile remote file path, this has to be a full qualified path
+ * @param localFile This is the local file to copy, this can be a directory too
+ * @throws SSHApiException
+ */
+ public void scpThirdParty(String remoteFileSorce, String remoteFileTarget) throws SSHApiException;
+
+ /**
+ * This will create directories in computing resources
+ * @param directoryPath the full qualified path for the directory user wants to create
+ * @throws SSHApiException throws during error
+ */
+ public void makeDirectory(String directoryPath) throws SSHApiException;
+
+
+ /**
+ * This will get the job description of a job which is there in the cluster
+ * if jbo is not available with the given ID it returns
+ * @param jobID jobId has to pass
+ * @return Returns full job description of the job which submitted successfully
+ * @throws SSHApiException throws exception during error
+ */
+ public JobDescriptor getJobDescriptorById(String jobID) throws SSHApiException;
+
+ /**
+ * This will delete the given job from the queue
+ *
+ * @param jobID jobId of the job which user wants to delete
+ * @return return the description of the deleted job
+ * @throws SSHApiException throws exception during error
+ */
+ public JobDescriptor cancelJob(String jobID) throws SSHApiException;
+
+ /**
+ * This will get the job status of the the job associated with this jobId
+ *
+ * @param jobID jobId of the job user want to get the status
+ * @return job status of the given jobID
+ * @throws SSHApiException throws exception during error
+ */
+ public JobStatus getJobStatus(String jobID) throws SSHApiException;
+ /**
+ * This will get the job status of the the job associated with this jobId
+ *
+ * @param jobName jobName of the job user want to get the status
+ * @return jobId of the given jobName
+ * @throws SSHApiException throws exception during error
+ */
+ public String getJobIdByJobName(String jobName, String userName) throws SSHApiException;
+
+ /**
+ * This method can be used to poll the jobstatuses based on the given
+ * user but we should pass the jobID list otherwise we will get unwanted
+ * job statuses which submitted by different middleware outside apache
+ * airavata with the same uername which we are not considering
+ * @param userName userName of the jobs which required to get the status
+ * @param jobIDs precises set of jobIDs
+ * @return
+ */
+ public void getJobStatuses(String userName,Map<String,JobStatus> jobIDs)throws SSHApiException;
+ /**
+ * This will list directories in computing resources
+ * @param directoryPath the full qualified path for the directory user wants to create
+ * @throws SSHApiException throws during error
+ */
+ public List<String> listDirectory(String directoryPath) throws SSHApiException;
+
+ /**
+ * This method can be used to get created ssh session
+ * to reuse the created session.
+ * @throws SSHApiException
+ */
+ public Session getSession() throws SSHApiException;
+
+ /**
+ * This method can be used to close the connections initialized
+ * to handle graceful shutdown of the system
+ * @throws SSHApiException
+ */
+ public void disconnect() throws SSHApiException;
+
+ /**
+ * This gives the server Info
+ * @return
+ */
+ public ServerInfo getServerInfo();
+
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java
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diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java
new file mode 100644
index 0000000..024c53d
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java
@@ -0,0 +1,278 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.ssh.api;
+
+import com.jcraft.jsch.*;
+import org.apache.airavata.gfac.ssh.api.authentication.*;
+import org.apache.airavata.gfac.ssh.config.ConfigReader;
+import org.apache.airavata.gfac.ssh.jsch.ExtendedJSch;
+import org.apache.airavata.gfac.ssh.util.SSHAPIUIKeyboardInteractive;
+import org.apache.airavata.gfac.ssh.util.SSHKeyPasswordHandler;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * This is a generic class which take care of command execution
+ * in a shell, this is used through out the other places of the API.
+ */
+public class CommandExecutor {
+ static {
+ JSch.setConfig("gssapi-with-mic.x509", "org.apache.airavata.gfac.ssh.GSSContextX509");
+ JSch.setConfig("userauth.gssapi-with-mic", "com.jcraft.jsch.UserAuthGSSAPIWithMICGSSCredentials");
+ JSch jSch = new JSch();
+ }
+
+ private static final Logger log = LoggerFactory.getLogger(CommandExecutor.class);
+ public static final String X509_CERT_DIR = "X509_CERT_DIR";
+
+ /**
+ * This will execute the given command with given session and session is not closed at the end.
+ *
+ * @param commandInfo
+ * @param session
+ * @param commandOutput
+ * @throws SSHApiException
+ */
+ public static Session executeCommand(CommandInfo commandInfo, Session session,
+ CommandOutput commandOutput) throws SSHApiException {
+
+ String command = commandInfo.getCommand();
+
+ Channel channel = null;
+ try {
+ if (!session.isConnected()) {
+ session.connect();
+ }
+ channel = session.openChannel("exec");
+ ((ChannelExec) channel).setCommand(command);
+ } catch (JSchException e) {
+// session.disconnect();
+
+ throw new SSHApiException("Unable to execute command - ", e);
+ }
+
+ channel.setInputStream(null);
+ ((ChannelExec) channel).setErrStream(commandOutput.getStandardError());
+ try {
+ channel.connect();
+ } catch (JSchException e) {
+
+ channel.disconnect();
+// session.disconnect();
+ throw new SSHApiException("Unable to retrieve command output. Command - " + command, e);
+ }
+
+
+ commandOutput.onOutput(channel);
+ //Only disconnecting the channel, session can be reused
+ channel.disconnect();
+ return session;
+ }
+
+ /**
+ * This will not reuse any session, it will create the session and close it at the end
+ *
+ * @param commandInfo Encapsulated information about command. E.g :- executable name
+ * parameters etc ...
+ * @param serverInfo The SSHing server information.
+ * @param authenticationInfo Security data needs to be communicated with remote server.
+ * @param commandOutput The output of the command.
+ * @param configReader configuration required for ssh/gshissh connection
+ * @throws SSHApiException throw exception when error occurs
+ */
+ public static void executeCommand(CommandInfo commandInfo, ServerInfo serverInfo,
+ AuthenticationInfo authenticationInfo,
+ CommandOutput commandOutput, ConfigReader configReader) throws SSHApiException {
+
+ if (authenticationInfo instanceof GSIAuthenticationInfo) {
+ System.setProperty(X509_CERT_DIR, (String) ((GSIAuthenticationInfo)authenticationInfo).getProperties().
+ get("X509_CERT_DIR"));
+ }
+
+
+ JSch jsch = new ExtendedJSch();
+
+ log.debug("Connecting to server - " + serverInfo.getHost() + ":" + serverInfo.getPort() + " with user name - "
+ + serverInfo.getUserName());
+
+ Session session;
+
+ try {
+ session = jsch.getSession(serverInfo.getUserName(), serverInfo.getHost(), serverInfo.getPort());
+ } catch (JSchException e) {
+ throw new SSHApiException("An exception occurred while creating SSH session." +
+ "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ }
+
+ java.util.Properties config = configReader.getProperties();
+ session.setConfig(config);
+
+ //=============================================================
+ // Handling vanilla SSH pieces
+ //=============================================================
+ if (authenticationInfo instanceof SSHPasswordAuthentication) {
+ String password = ((SSHPasswordAuthentication) authenticationInfo).
+ getPassword(serverInfo.getUserName(), serverInfo.getHost());
+
+ session.setUserInfo(new SSHAPIUIKeyboardInteractive(password));
+
+ // TODO figure out why we need to set password to session
+ session.setPassword(password);
+
+ } else if (authenticationInfo instanceof SSHPublicKeyFileAuthentication) {
+ SSHPublicKeyFileAuthentication sshPublicKeyFileAuthentication
+ = (SSHPublicKeyFileAuthentication)authenticationInfo;
+
+ String privateKeyFile = sshPublicKeyFileAuthentication.
+ getPrivateKeyFile(serverInfo.getUserName(), serverInfo.getHost());
+
+ logDebug("The private key file for vanilla SSH " + privateKeyFile);
+
+ String publicKeyFile = sshPublicKeyFileAuthentication.
+ getPrivateKeyFile(serverInfo.getUserName(), serverInfo.getHost());
+
+ logDebug("The public key file for vanilla SSH " + publicKeyFile);
+
+ Identity identityFile;
+
+ try {
+ identityFile = GSISSHIdentityFile.newInstance(privateKeyFile, null, jsch);
+ } catch (JSchException e) {
+ throw new SSHApiException("An exception occurred while initializing keys using files. " +
+ "(private key and public key)." +
+ "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName() + " private key file - " + privateKeyFile + ", public key file - " +
+ publicKeyFile, e);
+ }
+
+ // Add identity to identity repository
+ GSISSHIdentityRepository identityRepository = new GSISSHIdentityRepository(jsch);
+ identityRepository.add(identityFile);
+
+ // Set repository to session
+ session.setIdentityRepository(identityRepository);
+
+ // Set the user info
+ SSHKeyPasswordHandler sshKeyPasswordHandler
+ = new SSHKeyPasswordHandler((SSHKeyAuthentication)authenticationInfo);
+
+ session.setUserInfo(sshKeyPasswordHandler);
+
+ } else if (authenticationInfo instanceof SSHPublicKeyAuthentication) {
+
+ SSHPublicKeyAuthentication sshPublicKeyAuthentication
+ = (SSHPublicKeyAuthentication)authenticationInfo;
+
+ Identity identityFile;
+
+ try {
+ String name = serverInfo.getUserName() + "_" + serverInfo.getHost();
+ identityFile = GSISSHIdentityFile.newInstance(name,
+ sshPublicKeyAuthentication.getPrivateKey(serverInfo.getUserName(), serverInfo.getHost()),
+ sshPublicKeyAuthentication.getPublicKey(serverInfo.getUserName(), serverInfo.getHost()), jsch);
+ } catch (JSchException e) {
+ throw new SSHApiException("An exception occurred while initializing keys using byte arrays. " +
+ "(private key and public key)." +
+ "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ }
+
+ // Add identity to identity repository
+ GSISSHIdentityRepository identityRepository = new GSISSHIdentityRepository(jsch);
+ identityRepository.add(identityFile);
+
+ // Set repository to session
+ session.setIdentityRepository(identityRepository);
+
+ // Set the user info
+ SSHKeyPasswordHandler sshKeyPasswordHandler
+ = new SSHKeyPasswordHandler((SSHKeyAuthentication)authenticationInfo);
+
+ session.setUserInfo(sshKeyPasswordHandler);
+
+ }
+
+ // Not a good way, but we dont have any choice
+ if (session instanceof ExtendedSession) {
+ if (authenticationInfo instanceof GSIAuthenticationInfo) {
+ ((ExtendedSession) session).setAuthenticationInfo((GSIAuthenticationInfo)authenticationInfo);
+ }
+ }
+
+ try {
+ session.connect();
+ } catch (JSchException e) {
+ throw new SSHApiException("An exception occurred while connecting to server." +
+ "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ }
+
+ String command = commandInfo.getCommand();
+
+ Channel channel;
+ try {
+ channel = session.openChannel("exec");
+ ((ChannelExec) channel).setCommand(command);
+ } catch (JSchException e) {
+// session.disconnect();
+
+ throw new SSHApiException("Unable to execute command - " + command +
+ " on server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ }
+
+
+ channel.setInputStream(null);
+ ((ChannelExec) channel).setErrStream(commandOutput.getStandardError());
+
+ try {
+ channel.connect();
+ } catch (JSchException e) {
+
+ channel.disconnect();
+// session.disconnect();
+
+ throw new SSHApiException("Unable to retrieve command output. Command - " + command +
+ " on server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ }
+
+ commandOutput.onOutput(channel);
+
+ channel.disconnect();
+// session.disconnect();
+ }
+
+ private static void logDebug(String message) {
+ if (log.isDebugEnabled()) {
+ log.debug(message);
+ }
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandInfo.java
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diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandInfo.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandInfo.java
new file mode 100644
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+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandInfo.java
@@ -0,0 +1,34 @@
+package org.apache.airavata.gfac.ssh.api;/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+/**
+ * Encapsulates information about
+ */
+public interface CommandInfo {
+
+ /**
+ * Gets the executable command as a string.
+ * @return String encoded command. Should be able to execute
+ * directly on remote shell. Should includes appropriate parameters.
+ */
+ String getCommand();
+
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandOutput.java
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diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandOutput.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandOutput.java
new file mode 100644
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+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandOutput.java
@@ -0,0 +1,49 @@
+package org.apache.airavata.gfac.ssh.api;/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+
+import com.jcraft.jsch.Channel;
+
+import java.io.OutputStream;
+
+/**
+ * Output of a certain command. TODO rethink
+ */
+public interface CommandOutput {
+
+ /**
+ * Gets the output of the command as a stream.
+ * @param channel Command output as a stream.
+ */
+ void onOutput(Channel channel);
+
+ /**
+ * Gets standard error as a output stream.
+ * @return Command error as a stream.
+ */
+ OutputStream getStandardError();
+
+ /**
+ * The command exit code.
+ * @param code The program exit code
+ */
+ void exitCode(int code);
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Core.java
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diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Core.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Core.java
new file mode 100644
index 0000000..67dd043
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Core.java
@@ -0,0 +1,59 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.ssh.api;
+
+import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
+
+/**
+ * This represents a CPU core of a machine in the cluster
+ */
+public class Core {
+ private JobDescriptor job;
+ private String id;
+
+ public Core(String id) {
+ this.id = id;
+ this.job = null;
+ }
+
+ /**
+ * @return core's id
+ */
+ public String getId() {
+ return id;
+ }
+
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ /**
+ * @return job running on the core
+ */
+ public JobDescriptor getJob() {
+ return job;
+ }
+
+ public void setJob(JobDescriptor job) {
+ this.job = job;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Node.java
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diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Node.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Node.java
new file mode 100644
index 0000000..1515f39
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Node.java
@@ -0,0 +1,104 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.ssh.api;
+
+import java.util.HashMap;
+
+public class Node {
+ private String Name;
+ private Core[] Cores;
+ private String state;
+ private HashMap<String, String> status;
+ private String np;
+ private String ntype;
+
+ /**
+ * @return the machine's name
+ */
+ public String getName() {
+ return Name;
+ }
+
+ public void setName(String Name) {
+ this.Name = Name;
+ }
+
+ /**
+ * @return machine cores as an array
+ */
+ public Core[] getCores() {
+ return Cores;
+ }
+
+ public void setCores(Core[] Cores) {
+ this.Cores = Cores;
+ }
+
+
+ /**
+ * @return the machine state
+ */
+ public String getState() {
+ return state;
+ }
+
+ public void setState(String state) {
+ this.state = state;
+ }
+
+ /**
+ * @return the status
+ */
+ public HashMap<String, String> getStatus() {
+ return status;
+ }
+
+ public void setStatus(HashMap<String, String> status) {
+ this.setStatus(status);
+ }
+
+
+ /**
+ * @return the number of cores in the machine
+ */
+ public String getNp() {
+ return np;
+ }
+
+
+ public void setNp(String np) {
+ this.np = np;
+ }
+
+ /**
+ * @return the ntype of the machine
+ */
+ public String getNtype() {
+ return ntype;
+ }
+
+
+ public void setNtype(String ntype) {
+ this.ntype = ntype;
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/SSHApiException.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/SSHApiException.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/SSHApiException.java
new file mode 100644
index 0000000..f78825b
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/SSHApiException.java
@@ -0,0 +1,36 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.gfac.ssh.api;
+
+/**
+ * An exception class to wrap SSH command execution related errors.
+ */
+public class SSHApiException extends Exception {
+
+ public SSHApiException(String message) {
+ super(message);
+ }
+
+ public SSHApiException(String message, Exception e) {
+ super(message, e);
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/ServerInfo.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/ServerInfo.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/ServerInfo.java
new file mode 100644
index 0000000..d3c2160
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/ServerInfo.java
@@ -0,0 +1,65 @@
+package org.apache.airavata.gfac.ssh.api;/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+/**
+ * Encapsulate server information.
+ */
+public class ServerInfo {
+
+ private String host;
+ private String userName;
+ private int port = 22;
+
+ public ServerInfo(String userName, String host) {
+ this.userName = userName;
+ this.host = host;
+ }
+
+ public ServerInfo(String userName,String host, int port) {
+ this.host = host;
+ this.userName = userName;
+ this.port = port;
+ }
+
+ public String getHost() {
+ return host;
+ }
+
+ public void setHost(String host) {
+ this.host = host;
+ }
+
+ public String getUserName() {
+ return userName;
+ }
+
+ public void setUserName(String userName) {
+ this.userName = userName;
+ }
+
+ public int getPort() {
+ return port;
+ }
+
+ public void setPort(int port) {
+ this.port = port;
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobDescriptor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobDescriptor.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobDescriptor.java
new file mode 100644
index 0000000..7e936ec
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobDescriptor.java
@@ -0,0 +1,473 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.ssh.api.job;
+
+import org.apache.airavata.gfac.ssh.api.CommandOutput;
+import org.apache.airavata.gfac.ssh.util.CommonUtils;
+import org.apache.airavata.gfac.ssh.x2012.x12.*;
+import org.apache.xmlbeans.XmlException;
+
+import java.util.List;
+
+/**
+ * This class define a job with required parameters, based on this configuration API is generating a Pbs script and
+ * submit the job to the computing resource
+ */
+public class JobDescriptor {
+
+ private JobDescriptorDocument jobDescriptionDocument;
+
+
+ public JobDescriptor() {
+ jobDescriptionDocument = JobDescriptorDocument.Factory.newInstance();
+ jobDescriptionDocument.addNewJobDescriptor();
+ }
+
+ public JobDescriptor(JobDescriptorDocument jobDescriptorDocument) {
+ this.jobDescriptionDocument = jobDescriptorDocument;
+ }
+
+
+ public JobDescriptor(CommandOutput commandOutput) {
+ jobDescriptionDocument = JobDescriptorDocument.Factory.newInstance();
+ jobDescriptionDocument.addNewJobDescriptor();
+ }
+
+
+ public String toXML() {
+ return jobDescriptionDocument.xmlText();
+ }
+
+ public JobDescriptorDocument getJobDescriptorDocument() {
+ return this.jobDescriptionDocument;
+ }
+
+ /**
+ * With new app catalog thrift object integration, we don't use this
+ * @param xml
+ * @return
+ * @throws XmlException
+ */
+ @Deprecated
+ public static JobDescriptor fromXML(String xml)
+ throws XmlException {
+ JobDescriptorDocument parse = JobDescriptorDocument.Factory
+ .parse(xml);
+ JobDescriptor jobDescriptor = new JobDescriptor(parse);
+ return jobDescriptor;
+ }
+
+
+ //todo write bunch of setter getters to set and get jobdescription parameters
+ public void setWorkingDirectory(String workingDirectory) {
+ this.getJobDescriptorDocument().getJobDescriptor().setWorkingDirectory(workingDirectory);
+ }
+
+ public String getWorkingDirectory() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory();
+ }
+
+ public void setShellName(String shellName) {
+ this.getJobDescriptorDocument().getJobDescriptor().setShellName(shellName);
+ }
+
+ public void setJobName(String name) {
+ this.getJobDescriptorDocument().getJobDescriptor().setJobName(name);
+ }
+
+ public void setExecutablePath(String name) {
+ this.getJobDescriptorDocument().getJobDescriptor().setExecutablePath(name);
+ }
+
+ public void setAllEnvExport(boolean name) {
+ this.getJobDescriptorDocument().getJobDescriptor().setAllEnvExport(name);
+ }
+
+ public void setMailOptions(String name) {
+ this.getJobDescriptorDocument().getJobDescriptor().setMailOptions(name);
+ }
+
+ public void setStandardOutFile(String name) {
+ this.getJobDescriptorDocument().getJobDescriptor().setStandardOutFile(name);
+ }
+
+ public void setStandardErrorFile(String name) {
+ this.getJobDescriptorDocument().getJobDescriptor().setStandardErrorFile(name);
+ }
+
+ public void setNodes(int name) {
+ this.getJobDescriptorDocument().getJobDescriptor().setNodes(name);
+ }
+
+ public void setProcessesPerNode(int name) {
+ this.getJobDescriptorDocument().getJobDescriptor().setProcessesPerNode(name);
+ }
+
+ public String getOutputDirectory() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getOutputDirectory();
+ }
+
+ public String getInputDirectory() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getInputDirectory();
+ }
+ public void setOutputDirectory(String name) {
+ this.getJobDescriptorDocument().getJobDescriptor().setOutputDirectory(name);
+ }
+
+ public void setInputDirectory(String name) {
+ this.getJobDescriptorDocument().getJobDescriptor().setInputDirectory(name);
+ }
+
+ /**
+ * Users can pass the minute count for maxwalltime
+ * @param minutes
+ */
+ public void setMaxWallTime(String minutes) {
+ this.getJobDescriptorDocument().getJobDescriptor().setMaxWallTime(
+ CommonUtils.maxWallTimeCalculator(Integer.parseInt(minutes)));
+
+ }
+
+
+ public void setMaxWallTimeForLSF(String minutes) {
+ this.getJobDescriptorDocument().getJobDescriptor().setMaxWallTime(
+ CommonUtils.maxWallTimeCalculatorForLSF(Integer.parseInt(minutes)));
+
+ }
+ public void setAcountString(String name) {
+ this.getJobDescriptorDocument().getJobDescriptor().setAcountString(name);
+ }
+
+ public void setInputValues(List<String> inputValue) {
+ InputList inputList = this.getJobDescriptorDocument().getJobDescriptor().addNewInputs();
+ inputList.setInputArray(inputValue.toArray(new String[inputValue.size()]));
+ }
+
+ public void setJobID(String jobID) {
+ this.getJobDescriptorDocument().getJobDescriptor().setJobID(jobID);
+ }
+
+ public void setQueueName(String queueName) {
+ this.getJobDescriptorDocument().getJobDescriptor().setQueueName(queueName);
+ }
+
+ public void setStatus(String queueName) {
+ this.getJobDescriptorDocument().getJobDescriptor().setStatus(queueName);
+ }
+
+ public void setAfterAnyList(String[] afterAnyList) {
+ AfterAnyList afterAny = this.getJobDescriptorDocument().getJobDescriptor().addNewAfterAny();
+ afterAny.setAfterAnyArray(afterAnyList);
+ }
+
+ public void setAfterOKList(String[] afterOKList) {
+ AfterOKList afterAnyList = this.getJobDescriptorDocument().getJobDescriptor().addNewAfterOKList();
+ afterAnyList.setAfterOKListArray(afterOKList);
+ }
+ public void setCTime(String cTime) {
+ this.getJobDescriptorDocument().getJobDescriptor().setCTime(cTime);
+ }
+ public void setQTime(String qTime) {
+ this.getJobDescriptorDocument().getJobDescriptor().setQTime(qTime);
+ }
+ public void setMTime(String mTime) {
+ this.getJobDescriptorDocument().getJobDescriptor().setMTime(mTime);
+ }
+ public void setSTime(String sTime) {
+ this.getJobDescriptorDocument().getJobDescriptor().setSTime(sTime);
+ }
+ public void setCompTime(String compTime) {
+ this.getJobDescriptorDocument().getJobDescriptor().setCompTime(compTime);
+ }
+ public void setOwner(String owner) {
+ this.getJobDescriptorDocument().getJobDescriptor().setOwner(owner);
+ }
+ public void setExecuteNode(String executeNode) {
+ this.getJobDescriptorDocument().getJobDescriptor().setExecuteNode(executeNode);
+ }
+ public void setEllapsedTime(String ellapsedTime) {
+ this.getJobDescriptorDocument().getJobDescriptor().setEllapsedTime(ellapsedTime);
+ }
+
+ public void setUsedCPUTime(String usedCPUTime) {
+ this.getJobDescriptorDocument().getJobDescriptor().setUsedCPUTime(usedCPUTime);
+ }
+ public void setCPUCount(int usedCPUTime) {
+ this.getJobDescriptorDocument().getJobDescriptor().setCpuCount(usedCPUTime);
+ }
+ public void setUsedMemory(String usedMemory) {
+ this.getJobDescriptorDocument().getJobDescriptor().setUsedMem(usedMemory);
+ }
+ public void setVariableList(String variableList) {
+ this.getJobDescriptorDocument().getJobDescriptor().setVariableList(variableList);
+ }
+ public void setSubmitArgs(String submitArgs) {
+ this.getJobDescriptorDocument().getJobDescriptor().setSubmitArgs(submitArgs);
+ }
+
+ public void setPreJobCommands(String[] commands){
+ if(this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands() == null){
+ this.getJobDescriptorDocument().getJobDescriptor().addNewPreJobCommands();
+ }
+ this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands().setCommandArray(commands);
+ }
+
+ public void setPostJobCommands(String[] commands){
+ if(this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands() == null){
+ this.getJobDescriptorDocument().getJobDescriptor().addNewPostJobCommands();
+ }
+ this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands().setCommandArray(commands);
+ }
+
+ public void setModuleLoadCommands(String[] commands) {
+ if (this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands() == null) {
+ this.getJobDescriptorDocument().getJobDescriptor().addNewModuleLoadCommands();
+ }
+ this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands().setCommandArray(commands);
+ }
+
+ public void addModuleLoadCommands(String command) {
+ if (this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands() == null) {
+ this.getJobDescriptorDocument().getJobDescriptor().addNewModuleLoadCommands();
+ }
+ this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands().addCommand(command);
+ }
+
+ public void addPreJobCommand(String command){
+ if(this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands() == null){
+ this.getJobDescriptorDocument().getJobDescriptor().addNewPreJobCommands();
+ }
+ this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands().addCommand(command);
+ }
+
+ public void addPostJobCommand(String command){
+ if(this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands() == null){
+ this.getJobDescriptorDocument().getJobDescriptor().addNewPostJobCommands();
+ }
+ this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands().addCommand(command);
+ }
+
+ public void setPartition(String partition){
+ this.getJobDescriptorDocument().getJobDescriptor().setPartition(partition);
+ }
+
+ public void setUserName(String userName){
+ this.getJobDescriptorDocument().getJobDescriptor().setUserName(userName);
+ }
+ public void setNodeList(String nodeList){
+ this.getJobDescriptorDocument().getJobDescriptor().setNodeList(nodeList);
+ }
+ public void setJobSubmitter(String jobSubmitter){
+ this.getJobDescriptorDocument().getJobDescriptor().setJobSubmitterCommand(jobSubmitter);
+ }
+ public String getNodeList(){
+ return this.getJobDescriptorDocument().getJobDescriptor().getNodeList();
+ }
+ public String getExecutablePath() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getExecutablePath();
+ }
+
+ public boolean getAllEnvExport() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getAllEnvExport();
+ }
+
+ public String getMailOptions() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getMailOptions();
+ }
+
+ public String getStandardOutFile() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile();
+ }
+
+ public String getStandardErrorFile() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile();
+ }
+
+ public int getNodes(int name) {
+ return this.getJobDescriptorDocument().getJobDescriptor().getNodes();
+ }
+
+ public int getCPUCount(int name) {
+ return this.getJobDescriptorDocument().getJobDescriptor().getCpuCount();
+ }
+
+ public int getProcessesPerNode() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getProcessesPerNode();
+ }
+
+ public String getMaxWallTime() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getMaxWallTime();
+ }
+
+ public String getAcountString() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getAcountString();
+ }
+
+ public String[] getInputValues() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getInputs().getInputArray();
+ }
+
+ public String getJobID() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
+ }
+
+ public String getQueueName() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getQueueName();
+ }
+
+ public String getStatus() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getStatus();
+ }
+
+ public String[] getAfterAnyList() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getAfterAny().getAfterAnyArray();
+ }
+
+ public String[] getAfterOKList() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getAfterOKList().getAfterOKListArray();
+ }
+ public String getCTime() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getCTime();
+ }
+ public String getQTime() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getQTime();
+ }
+ public String getMTime() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getMTime();
+ }
+ public String getSTime() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getSTime();
+ }
+ public String getCompTime() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getCompTime();
+ }
+ public String getOwner() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getOwner();
+ }
+ public String getExecuteNode() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getExecuteNode();
+ }
+ public String getEllapsedTime() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getEllapsedTime();
+ }
+
+ public String getUsedCPUTime() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getUsedCPUTime();
+ }
+
+ public String getUsedMemory() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getUsedMem();
+ }
+ public void getShellName() {
+ this.getJobDescriptorDocument().getJobDescriptor().getShellName();
+ }
+
+ public String getJobName() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getJobName();
+ }
+
+ public String getJobId() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
+ }
+
+
+ public String getVariableList() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
+ }
+ public String getSubmitArgs() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
+ }
+
+ public String[] getPostJobCommands(){
+ if(this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands() != null) {
+ return this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands().getCommandArray();
+ }
+ return null;
+ }
+
+ public String[] getModuleCommands() {
+ if (this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands() != null) {
+ return this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands().getCommandArray();
+ }
+ return null;
+ }
+
+ public String[] getPreJobCommands(){
+ if(this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands() != null) {
+ return this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands().getCommandArray();
+ }
+ return null;
+ }
+
+ public String getJobSubmitterCommand(){
+ return this.getJobDescriptorDocument().getJobDescriptor().getJobSubmitterCommand();
+ }
+
+ public String getPartition(){
+ return this.getJobDescriptorDocument().getJobDescriptor().getPartition();
+ }
+
+ public String getUserName(){
+ return this.getJobDescriptorDocument().getJobDescriptor().getUserName();
+ }
+
+ public void setCallBackIp(String ip){
+ this.jobDescriptionDocument.getJobDescriptor().setCallBackIp(ip);
+ }
+
+ public void setCallBackPort(String ip){
+ this.jobDescriptionDocument.getJobDescriptor().setCallBackPort(ip);
+ }
+
+
+ public String getCallBackIp(){
+ return this.jobDescriptionDocument.getJobDescriptor().getCallBackIp();
+ }
+ public String getCallBackPort(){
+ return this.jobDescriptionDocument.getJobDescriptor().getCallBackPort();
+ }
+
+ public void setMailType(String emailType) {
+ this.getJobDescriptorDocument().getJobDescriptor().setMailType(emailType);
+ }
+
+ public String getMailType() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getMailType();
+ }
+ public void setMailAddress(String emailAddress) {
+ this.getJobDescriptorDocument().getJobDescriptor().setMailAddress(emailAddress);
+ }
+
+ public String getMailAddress() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getMailAddress();
+ }
+
+ public String getChassisName() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getChassisName();
+ }
+
+ public void setChassisName(String chassisName){
+ this.getJobDescriptorDocument().getJobDescriptor().setChassisName(chassisName);
+ }
+
+
+}
+
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobManagerConfiguration.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobManagerConfiguration.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobManagerConfiguration.java
new file mode 100644
index 0000000..d58a994
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobManagerConfiguration.java
@@ -0,0 +1,51 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+package org.apache.airavata.gfac.ssh.api.job;
+
+import org.apache.airavata.gfac.ssh.impl.RawCommandInfo;
+
+public interface JobManagerConfiguration {
+
+ public RawCommandInfo getCancelCommand(String jobID);
+
+ public String getJobDescriptionTemplateName();
+
+ public RawCommandInfo getMonitorCommand(String jobID);
+
+ public RawCommandInfo getUserBasedMonitorCommand(String userName);
+
+ public RawCommandInfo getJobIdMonitorCommand(String jobName , String userName);
+
+ public String getScriptExtension();
+
+ public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath);
+
+ public OutputParser getParser();
+
+ public String getInstalledPath();
+
+ public String getBaseCancelCommand();
+
+ public String getBaseMonitorCommand();
+
+ public String getBaseSubmitCommand();
+
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobType.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobType.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobType.java
new file mode 100644
index 0000000..556f4ef
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobType.java
@@ -0,0 +1,32 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.ssh.api.job;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: lahirugunathilake
+ * Date: 8/22/13
+ * Time: 7:19 AM
+ * To change this template use File | Settings | File Templates.
+ */
+public enum JobType {
+ SERIAL, SINGLE, MPI, MULTIPLE, CONDOR
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFJobConfiguration.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFJobConfiguration.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFJobConfiguration.java
new file mode 100644
index 0000000..f9c7f33
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFJobConfiguration.java
@@ -0,0 +1,121 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.ssh.api.job;
+
+import org.apache.airavata.gfac.ssh.impl.RawCommandInfo;
+import org.apache.commons.io.FilenameUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+
+public class LSFJobConfiguration implements JobManagerConfiguration {
+ private final static Logger logger = LoggerFactory.getLogger(LSFJobConfiguration.class);
+
+ private String jobDescriptionTemplateName;
+
+ private String scriptExtension;
+
+ private String installedPath;
+
+ private OutputParser parser;
+
+ public LSFJobConfiguration(){
+ // this can be used to construct and use setter methods to set all the params in order
+ }
+ public LSFJobConfiguration(String jobDescriptionTemplateName,
+ String scriptExtension,String installedPath,OutputParser parser) {
+ this.jobDescriptionTemplateName = jobDescriptionTemplateName;
+ this.scriptExtension = scriptExtension;
+ this.parser = parser;
+ if (installedPath.endsWith("/") || installedPath.isEmpty()) {
+ this.installedPath = installedPath;
+ } else {
+ this.installedPath = installedPath + "/";
+ }
+ }
+
+ @Override
+ public RawCommandInfo getCancelCommand(String jobID) {
+ return new RawCommandInfo(this.installedPath + "bkill " + jobID);
+ }
+
+ @Override
+ public String getJobDescriptionTemplateName() {
+ return jobDescriptionTemplateName;
+ }
+
+ @Override
+ public RawCommandInfo getMonitorCommand(String jobID) {
+ return new RawCommandInfo(this.installedPath + "bjobs " + jobID);
+ }
+
+ @Override
+ public RawCommandInfo getUserBasedMonitorCommand(String userName) {
+ return new RawCommandInfo(this.installedPath + "bjobs -u " + userName);
+ }
+
+ @Override
+ public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
+ return new RawCommandInfo(this.installedPath + "bjobs -J " + jobName);
+ }
+
+ @Override
+ public String getScriptExtension() {
+ return scriptExtension;
+ }
+
+ @Override
+ public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath) {
+ return new RawCommandInfo(this.installedPath + "bsub < " +
+ workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
+ }
+
+ @Override
+ public OutputParser getParser() {
+ return parser;
+ }
+
+ public void setParser(OutputParser parser) {
+ this.parser = parser;
+ }
+
+ @Override
+ public String getInstalledPath() {
+ return installedPath;
+ }
+
+
+ @Override
+ public String getBaseCancelCommand() {
+ return "bkill";
+ }
+
+ @Override
+ public String getBaseMonitorCommand() {
+ return "bjobs";
+ }
+
+ @Override
+ public String getBaseSubmitCommand() {
+ return "bsub";
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFOutputParser.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFOutputParser.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFOutputParser.java
new file mode 100644
index 0000000..c6dea17
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFOutputParser.java
@@ -0,0 +1,130 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.ssh.api.job;
+
+import org.apache.airavata.gfac.ssh.api.SSHApiException;
+import org.apache.airavata.gfac.ssh.impl.JobStatus;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+public class LSFOutputParser implements OutputParser {
+ private final static Logger logger = LoggerFactory.getLogger(LSFOutputParser.class);
+
+ @Override
+ public void parseSingleJob(JobDescriptor jobDescriptor, String rawOutput) throws SSHApiException {
+ logger.debug(rawOutput);
+ //todo we need to implement this but we are not using it airavata runtime
+ // if someone is using the gsissh as a tool this will be useful to get a descriptive information about a single job
+ }
+
+ @Override
+ public String parseJobSubmission(String rawOutput) throws SSHApiException {
+ logger.debug(rawOutput);
+ return rawOutput.substring(rawOutput.indexOf("<")+1,rawOutput.indexOf(">"));
+ }
+
+ @Override
+ public JobStatus parseJobStatus(String jobID, String rawOutput) throws SSHApiException {
+ boolean jobFount = false;
+ logger.debug(rawOutput);
+ //todo this is not used anymore
+ return JobStatus.C;
+ }
+
+ @Override
+ public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput) throws SSHApiException {
+ logger.debug(rawOutput);
+
+ String[] info = rawOutput.split("\n");
+// int lastStop = 0;
+ for (String jobID : statusMap.keySet()) {
+ String jobName = jobID.split(",")[1];
+ boolean found = false;
+ for (int i = 0; i < info.length; i++) {
+ if (info[i].contains(jobName.substring(0,8))) {
+ // now starts processing this line
+ logger.info(info[i]);
+ String correctLine = info[i];
+ String[] columns = correctLine.split(" ");
+ List<String> columnList = new ArrayList<String>();
+ for (String s : columns) {
+ if (!"".equals(s)) {
+ columnList.add(s);
+ }
+ }
+// lastStop = i + 1;
+ try {
+ statusMap.put(jobID, JobStatus.valueOf(columnList.get(2)));
+ }catch(IndexOutOfBoundsException e){
+ statusMap.put(jobID, JobStatus.valueOf("U"));
+ }
+ found = true;
+ break;
+ }
+ }
+ if(!found)
+ logger.error("Couldn't find the status of the Job with JobName: " + jobName + "Job Id: " + jobID.split(",")[0]);
+ }
+ }
+
+ @Override
+ public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
+ String regJobId = "jobId";
+ Pattern pattern = Pattern.compile("(?=(?<" + regJobId + ">\\d+)\\s+\\w+\\s+" + jobName + ")"); // regex - look ahead and match
+ if (rawOutput != null) {
+ Matcher matcher = pattern.matcher(rawOutput);
+ if (matcher.find()) {
+ return matcher.group(regJobId);
+ } else {
+ logger.error("No match is found for JobName");
+ return null;
+ }
+ } else {
+ logger.error("Error: RawOutput shouldn't be null");
+ return null;
+ }
+ }
+
+ public static void main(String[] args) {
+ String test = "Job <2477982> is submitted to queue <short>.";
+ System.out.println(test.substring(test.indexOf("<")+1, test.indexOf(">")));
+ String test1 = "JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME\n" +
+ "2636607 lg11w RUN long ghpcc06 c11b02 *069656647 Mar 7 00:58\n" +
+ "2636582 lg11w RUN long ghpcc06 c02b01 2134490944 Mar 7 00:48";
+ Map<String, JobStatus> statusMap = new HashMap<String, JobStatus>();
+ statusMap.put("2477983,2134490944", JobStatus.U);
+ LSFOutputParser lsfOutputParser = new LSFOutputParser();
+ try {
+ lsfOutputParser.parseJobStatuses("cjh", statusMap, test1);
+ } catch (SSHApiException e) {
+ logger.error(e.getMessage(), e);
+ }
+ System.out.println(statusMap.get("2477983,2134490944"));
+
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/OutputParser.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/OutputParser.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/OutputParser.java
new file mode 100644
index 0000000..9730c33
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/OutputParser.java
@@ -0,0 +1,67 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.ssh.api.job;
+
+import org.apache.airavata.gfac.ssh.api.SSHApiException;
+import org.apache.airavata.gfac.ssh.impl.JobStatus;
+
+import java.util.Map;
+
+public interface OutputParser {
+
+ /**
+ * Tihs can be used to fill a jobdescriptor based on the output
+ * @param descriptor
+ * @return
+ */
+ public void parseSingleJob(JobDescriptor descriptor, String rawOutput)throws SSHApiException;
+
+ /**
+ * This can be used to parseSingleJob the result of a job submission to get the JobID
+ * @param rawOutput
+ * @return
+ */
+ public String parseJobSubmission(String rawOutput)throws SSHApiException;
+
+
+ /**
+ * This can be used to get the job status from the output
+ * @param jobID
+ * @param rawOutput
+ */
+ public JobStatus parseJobStatus(String jobID, String rawOutput)throws SSHApiException;
+
+ /**
+ * This can be used to parseSingleJob a big output and get multipleJob statuses
+ * @param statusMap list of status map will return and key will be the job ID
+ * @param rawOutput
+ */
+ public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput)throws SSHApiException;
+
+ /**
+ * filter the jobId value of given JobName from rawOutput
+ * @param jobName
+ * @param rawOutput
+ * @return
+ * @throws SSHApiException
+ */
+ public String parseJobId(String jobName, String rawOutput) throws SSHApiException;
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSJobConfiguration.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSJobConfiguration.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSJobConfiguration.java
new file mode 100644
index 0000000..0179e01
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSJobConfiguration.java
@@ -0,0 +1,119 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.ssh.api.job;
+
+import org.apache.airavata.gfac.ssh.impl.RawCommandInfo;
+import org.apache.commons.io.FilenameUtils;
+
+import java.io.File;
+
+public class PBSJobConfiguration implements JobManagerConfiguration {
+
+ private String jobDescriptionTemplateName;
+
+ private String scriptExtension;
+
+ private String installedPath;
+
+ private OutputParser parser;
+
+ public PBSJobConfiguration() {
+ // this can be used to construct and use setter methods to set all the params in order
+ }
+
+ public PBSJobConfiguration(String jobDescriptionTemplateName,
+ String scriptExtension, String installedPath, OutputParser parser) {
+ this.jobDescriptionTemplateName = jobDescriptionTemplateName;
+ this.scriptExtension = scriptExtension;
+ this.parser = parser;
+ if (installedPath.endsWith("/")) {
+ this.installedPath = installedPath;
+ } else {
+ this.installedPath = installedPath + "/";
+ }
+ }
+
+ public RawCommandInfo getCancelCommand(String jobID) {
+ return new RawCommandInfo(this.installedPath + "qdel " + jobID);
+ }
+
+ public String getJobDescriptionTemplateName() {
+ return jobDescriptionTemplateName;
+ }
+
+ public void setJobDescriptionTemplateName(String jobDescriptionTemplateName) {
+ this.jobDescriptionTemplateName = jobDescriptionTemplateName;
+ }
+
+ public RawCommandInfo getMonitorCommand(String jobID) {
+ return new RawCommandInfo(this.installedPath + "qstat -f " + jobID);
+ }
+
+ public String getScriptExtension() {
+ return scriptExtension;
+ }
+
+ public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath) {
+ return new RawCommandInfo(this.installedPath + "qsub " +
+ workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
+ }
+
+ public String getInstalledPath() {
+ return installedPath;
+ }
+
+ public void setInstalledPath(String installedPath) {
+ this.installedPath = installedPath;
+ }
+
+ public OutputParser getParser() {
+ return parser;
+ }
+
+ public void setParser(OutputParser parser) {
+ this.parser = parser;
+ }
+
+ public RawCommandInfo getUserBasedMonitorCommand(String userName) {
+ return new RawCommandInfo(this.installedPath + "qstat -u " + userName);
+ }
+
+ @Override
+ public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
+ // For PBS there is no option to get jobDetails by JobName, so we search with userName
+ return new RawCommandInfo(this.installedPath + "qstat -u " + userName);
+ }
+
+ @Override
+ public String getBaseCancelCommand() {
+ return "qdel";
+ }
+
+ @Override
+ public String getBaseMonitorCommand() {
+ return "qstat";
+ }
+
+ @Override
+ public String getBaseSubmitCommand() {
+ return "qsub ";
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSOutputParser.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSOutputParser.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSOutputParser.java
new file mode 100644
index 0000000..2f17787
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSOutputParser.java
@@ -0,0 +1,212 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.ssh.api.job;
+
+import org.apache.airavata.gfac.ssh.api.SSHApiException;
+import org.apache.airavata.gfac.ssh.impl.JobStatus;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+public class PBSOutputParser implements OutputParser {
+ private static final Logger log = LoggerFactory.getLogger(PBSOutputParser.class);
+
+ public void parseSingleJob(JobDescriptor jobDescriptor, String rawOutput) {
+ log.debug(rawOutput);
+ String[] info = rawOutput.split("\n");
+ String[] line;
+ for (int i = 0; i < info.length; i++) {
+ if (info[i].contains("=")) {
+ line = info[i].split("=", 2);
+ } else {
+ line = info[i].split(":", 2);
+ }
+ if (line.length >= 2) {
+ String header = line[0].trim();
+ log.debug("Header = " + header);
+ String value = line[1].trim();
+ log.debug("value = " + value);
+
+ if (header.equals("Variable_List")) {
+ while (info[i + 1].startsWith("\t")) {
+ value += info[i + 1];
+ i++;
+ }
+ value = value.replaceAll("\t", "");
+ jobDescriptor.setVariableList(value);
+ } else if ("Job Id".equals(header)) {
+ jobDescriptor.setJobID(value);
+ } else if ("Job_Name".equals(header)) {
+ jobDescriptor.setJobName(value);
+ } else if ("Account_Name".equals(header)) {
+ jobDescriptor.setAcountString(value);
+ } else if ("job_state".equals(header)) {
+ jobDescriptor.setStatus(value);
+ } else if ("Job_Owner".equals(header)) {
+ jobDescriptor.setOwner(value);
+ } else if ("resources_used.cput".equals(header)) {
+ jobDescriptor.setUsedCPUTime(value);
+ } else if ("resources_used.mem".equals(header)) {
+ jobDescriptor.setUsedMemory(value);
+ } else if ("resources_used.walltime".equals(header)) {
+ jobDescriptor.setEllapsedTime(value);
+ } else if ("job_state".equals(header)) {
+ jobDescriptor.setStatus(value);
+ } else if ("queue".equals(header))
+ jobDescriptor.setQueueName(value);
+ else if ("ctime".equals(header)) {
+ jobDescriptor.setCTime(value);
+ } else if ("qtime".equals(header)) {
+ jobDescriptor.setQTime(value);
+ } else if ("mtime".equals(header)) {
+ jobDescriptor.setMTime(value);
+ } else if ("start_time".equals(header)) {
+ jobDescriptor.setSTime(value);
+ } else if ("comp_time".equals(header)) {
+ jobDescriptor.setCompTime(value);
+ } else if ("exec_host".equals(header)) {
+ jobDescriptor.setExecuteNode(value);
+ } else if ("Output_Path".equals(header)) {
+ if (info[i + 1].contains("=") || info[i + 1].contains(":"))
+ jobDescriptor.setStandardOutFile(value);
+ else {
+ jobDescriptor.setStandardOutFile(value + info[i + 1].trim());
+ i++;
+ }
+ } else if ("Error_Path".equals(header)) {
+ if (info[i + 1].contains("=") || info[i + 1].contains(":"))
+ jobDescriptor.setStandardErrorFile(value);
+ else {
+ String st = info[i + 1].trim();
+ jobDescriptor.setStandardErrorFile(value + st);
+ i++;
+ }
+
+ } else if ("submit_args".equals(header)) {
+ while (i + 1 < info.length) {
+ if (info[i + 1].startsWith("\t")) {
+ value += info[i + 1];
+ i++;
+ } else
+ break;
+ }
+ value = value.replaceAll("\t", "");
+ jobDescriptor.setSubmitArgs(value);
+ }
+ }
+ }
+ }
+
+ public String parseJobSubmission(String rawOutput) {
+ log.debug(rawOutput);
+ return rawOutput; //In PBS stdout is going to be directly the jobID
+ }
+
+ public JobStatus parseJobStatus(String jobID, String rawOutput) {
+ boolean jobFount = false;
+ log.debug(rawOutput);
+ String[] info = rawOutput.split("\n");
+ String[] line = null;
+ int index = 0;
+ for (String anInfo : info) {
+ index++;
+ if (anInfo.contains("Job Id:")) {
+ if (anInfo.contains(jobID)) {
+ jobFount = true;
+ break;
+ }
+ }
+ }
+ if (jobFount) {
+ for (int i=index;i<info.length;i++) {
+ String anInfo = info[i];
+ if (anInfo.contains("=")) {
+ line = anInfo.split("=", 2);
+ if (line.length != 0) {
+ if (line[0].contains("job_state")) {
+ return JobStatus.valueOf(line[1].replaceAll(" ", ""));
+ }
+ }
+ }
+ }
+ }
+ return null;
+ }
+
+ public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput) {
+ log.debug(rawOutput);
+ String[] info = rawOutput.split("\n");
+// int lastStop = 0;
+ for (String jobID : statusMap.keySet()) {
+ String jobName = jobID.split(",")[1];
+ boolean found = false;
+ for (int i = 0; i < info.length; i++) {
+ if (info[i].contains(jobName.substring(0,8))) {
+ // now starts processing this line
+ log.info(info[i]);
+ String correctLine = info[i];
+ String[] columns = correctLine.split(" ");
+ List<String> columnList = new ArrayList<String>();
+ for (String s : columns) {
+ if (!"".equals(s)) {
+ columnList.add(s);
+ }
+ }
+// lastStop = i + 1;
+ try {
+ statusMap.put(jobID, JobStatus.valueOf(columnList.get(9)));
+ }catch(IndexOutOfBoundsException e){
+ statusMap.put(jobID, JobStatus.valueOf("U"));
+ }
+ found = true;
+ break;
+ }
+ }
+ if(!found)
+ log.error("Couldn't find the status of the Job with JobName: " + jobName + "Job Id: " + jobID.split(",")[0]);
+ }
+ }
+
+ @Override
+ public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
+ String regJobId = "jobId";
+ Pattern pattern = Pattern.compile("\\s*(?<" + regJobId + ">[^\\s]*).* " + jobName + " "); // regex , JOB_ID will come as first column
+ if (rawOutput != null) {
+ Matcher matcher = pattern.matcher(rawOutput);
+ if (matcher.find()) {
+ return matcher.group(regJobId);
+ } else {
+ log.error("No match is found for JobName");
+ return null;
+ }
+ } else {
+ log.error("Error: RawOutput shouldn't be null");
+ return null;
+ }
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmJobConfiguration.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmJobConfiguration.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmJobConfiguration.java
new file mode 100644
index 0000000..54d8f40
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmJobConfiguration.java
@@ -0,0 +1,117 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.ssh.api.job;
+
+import org.apache.airavata.gfac.ssh.impl.RawCommandInfo;
+import org.apache.commons.io.FilenameUtils;
+
+import java.io.File;
+
+public class SlurmJobConfiguration implements JobManagerConfiguration{
+
+ private String jobDescriptionTemplateName;
+
+ private String scriptExtension;
+
+ private String installedPath;
+
+ private OutputParser parser;
+
+ public SlurmJobConfiguration(){
+ // this can be used to construct and use setter methods to set all the params in order
+ }
+ public SlurmJobConfiguration(String jobDescriptionTemplateName,
+ String scriptExtension,String installedPath,OutputParser parser) {
+ this.jobDescriptionTemplateName = jobDescriptionTemplateName;
+ this.scriptExtension = scriptExtension;
+ this.parser = parser;
+ if (installedPath.endsWith("/")) {
+ this.installedPath = installedPath;
+ } else {
+ this.installedPath = installedPath + "/";
+ }
+ }
+
+ public RawCommandInfo getCancelCommand(String jobID) {
+ return new RawCommandInfo(this.installedPath + "scancel " + jobID);
+ }
+
+ public String getJobDescriptionTemplateName() {
+ return jobDescriptionTemplateName;
+ }
+
+ public void setJobDescriptionTemplateName(String jobDescriptionTemplateName) {
+ this.jobDescriptionTemplateName = jobDescriptionTemplateName;
+ }
+
+ public RawCommandInfo getMonitorCommand(String jobID) {
+ return new RawCommandInfo(this.installedPath + "squeue -j " + jobID);
+ }
+
+ public String getScriptExtension() {
+ return scriptExtension;
+ }
+
+ public RawCommandInfo getSubmitCommand(String workingDirectory,String pbsFilePath) {
+ return new RawCommandInfo(this.installedPath + "sbatch " +
+ workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
+ }
+
+ public String getInstalledPath() {
+ return installedPath;
+ }
+
+ public void setInstalledPath(String installedPath) {
+ this.installedPath = installedPath;
+ }
+
+ public OutputParser getParser() {
+ return parser;
+ }
+
+ public void setParser(OutputParser parser) {
+ this.parser = parser;
+ }
+
+ public RawCommandInfo getUserBasedMonitorCommand(String userName) {
+ return new RawCommandInfo(this.installedPath + "squeue -u " + userName);
+ }
+
+ @Override
+ public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
+ return new RawCommandInfo(this.installedPath + "squeue -n " + jobName + " -u " + userName);
+ }
+
+ @Override
+ public String getBaseCancelCommand() {
+ return "scancel";
+ }
+
+ @Override
+ public String getBaseMonitorCommand() {
+ return "squeue";
+ }
+
+ @Override
+ public String getBaseSubmitCommand() {
+ return "sbatch";
+ }
+}